Locus 1604

Sequence ID 3R_DroMel_CAF1
Location 4,620,260 – 4,620,350
Length 90
Max. P 0.906195
window2646 window2647

overview

Window 6

Location 4,620,260 – 4,620,350
Length 90
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 85.15
Mean single sequence MFE -26.27
Consensus MFE -18.20
Energy contribution -19.32
Covariance contribution 1.12
Combinations/Pair 1.23
Mean z-score -3.19
Structure conservation index 0.69
SVM decision value 0.38
SVM RNA-class probability 0.714928
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4620260 90 + 27905053
GGUAUAAA-----AGUGCAGAAGAUAUAGCAUAAUAUUUGCUUAACGCCCUUUGCCGA----UAUGGCAAGCAUUAGGGAAAUUGCUAUAUCGAAAUUG
.((((...-----.))))....(((((((((....((((.(((((.((...(((((..----...))))))).))))).)))))))))))))....... ( -26.20)
>DroSec_CAF1 19045 90 + 1
GGUAUGAA-----AGUGCAGAAGAUAUAGCAUAAUAUUUGCUUAACGCCCUUCGCCGA----UAUGGCAAGCAUUAGGGAAAUUGCUAUAUCGAAAUUG
.((((...-----.))))....(((((((((....((((.(((((.((.....(((..----...)))..)).))))).)))))))))))))....... ( -25.50)
>DroSim_CAF1 20308 90 + 1
GGUAUGAA-----AGUGCAGAAGAUAUAGCAUAAUAUUUGCUUAACGCCCUUUGCCGA----UAUGGCAAGCAUUAGGGAAAUUGCUAUAUCGAAAUUG
.((((...-----.))))....(((((((((....((((.(((((.((...(((((..----...))))))).))))).)))))))))))))....... ( -28.50)
>DroEre_CAF1 20166 81 + 1
GGUAUGAA-----AGUGCAGAAGAUAUUGCAUAAUAUUUAC---------CUUGCCGA----UAUGGCAAGCAUUAGGGAAAUUGCUAUAUCGAAAUUG
((((....-----.((((((......))))))......)))---------)....(((----((((((((.(......)...)))))))))))...... ( -22.20)
>DroYak_CAF1 20030 90 + 1
GGUAUGAA-----AGUGCAGAAGAUAUAGCAUAAUAUUUGCUUAACGCCCUUUGCCGA----UAUGGCAAGCAUUAAGGAAAUUGCUAUAUCGAAAUUG
.((((...-----.))))....(((((((((....((((.(((((.((...(((((..----...))))))).))))).)))))))))))))....... ( -28.80)
>DroAna_CAF1 19928 98 + 1
GGUCUCGAUGGUUAGGGUAUAAGAUAUGGCACAAUAUUUGCUU-UCGUCCUCCGCUGAUAGAUAGGACGAGCAUUAGUGAAAUUGCCAUAUCGAAAUUG
...(((........))).....(((((((((.....((..(((-(((((((...(.....)..))))))))....))..))..)))))))))....... ( -26.40)
>consensus
GGUAUGAA_____AGUGCAGAAGAUAUAGCAUAAUAUUUGCUUAACGCCCUUUGCCGA____UAUGGCAAGCAUUAGGGAAAUUGCUAUAUCGAAAUUG
.((((.........))))....(((((((((....((((.(((((.((...((((((.......)))))))).))))).)))))))))))))....... (-18.20 = -19.32 +   1.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,620,260 – 4,620,350
Length 90
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 85.15
Mean single sequence MFE -22.77
Consensus MFE -16.74
Energy contribution -17.88
Covariance contribution 1.14
Combinations/Pair 1.20
Mean z-score -3.74
Structure conservation index 0.74
SVM decision value 1.05
SVM RNA-class probability 0.906195
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4620260 90 - 27905053
CAAUUUCGAUAUAGCAAUUUCCCUAAUGCUUGCCAUA----UCGGCAAAGGGCGUUAAGCAAAUAUUAUGCUAUAUCUUCUGCACU-----UUUAUACC
.......(((((((((((((.(.(((((((((((...----..))))...))))))).).))))....))))))))).........-----........ ( -23.40)
>DroSec_CAF1 19045 90 - 1
CAAUUUCGAUAUAGCAAUUUCCCUAAUGCUUGCCAUA----UCGGCGAAGGGCGUUAAGCAAAUAUUAUGCUAUAUCUUCUGCACU-----UUCAUACC
.......(((((((((((((.(.(((((((((((...----..))))...))))))).).))))....))))))))).........-----........ ( -22.70)
>DroSim_CAF1 20308 90 - 1
CAAUUUCGAUAUAGCAAUUUCCCUAAUGCUUGCCAUA----UCGGCAAAGGGCGUUAAGCAAAUAUUAUGCUAUAUCUUCUGCACU-----UUCAUACC
.......(((((((((((((.(.(((((((((((...----..))))...))))))).).))))....))))))))).........-----........ ( -23.40)
>DroEre_CAF1 20166 81 - 1
CAAUUUCGAUAUAGCAAUUUCCCUAAUGCUUGCCAUA----UCGGCAAG---------GUAAAUAUUAUGCAAUAUCUUCUGCACU-----UUCAUACC
.......(((((.((((((.....))).((((((...----..))))))---------..........))).))))).........-----........ ( -14.70)
>DroYak_CAF1 20030 90 - 1
CAAUUUCGAUAUAGCAAUUUCCUUAAUGCUUGCCAUA----UCGGCAAAGGGCGUUAAGCAAAUAUUAUGCUAUAUCUUCUGCACU-----UUCAUACC
.......(((((((((((((.(((((((((((((...----..))))...))))))))).))))....))))))))).........-----........ ( -27.50)
>DroAna_CAF1 19928 98 - 1
CAAUUUCGAUAUGGCAAUUUCACUAAUGCUCGUCCUAUCUAUCAGCGGAGGACGA-AAGCAAAUAUUGUGCCAUAUCUUAUACCCUAACCAUCGAGACC
.......(((((((((..........((((((((((.((.......)))))))))-..))).......)))))))))...................... ( -24.93)
>consensus
CAAUUUCGAUAUAGCAAUUUCCCUAAUGCUUGCCAUA____UCGGCAAAGGGCGUUAAGCAAAUAUUAUGCUAUAUCUUCUGCACU_____UUCAUACC
.......(((((((((((((.(.(((((((((((.........)))))...)))))).).))))....)))))))))...................... (-16.74 = -17.88 +   1.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:40 2006